An analytical model was developed to assess the service time of the barrier system consisting of a two-layer cover system and a cut-off wall. The recursive method is used to evaluate the influence of the variable head loss boundary condition caused by the water infiltration. The impact of the types of cover systems and cut-off walls on the barrier system performance is assessed. The results show that cover system types are more likely to influence the long-time performance of barrier systems. Contaminant concentrations with H1* = 0.5 m and H2* = 0.3 m when t = 40 and 100 years are 1.17 and 1.42 times larger than those with H1* = H2* = 0.5 m, respectively. The decrease in hydraulic conductivity of cut-off wall and the increase in the thicknesses and retardation factors of it can also significantly improve the performance of barrier systems. Among all of the parameters, the cut-off wall thickness poses the most significant influence on the contaminant cumulative concentrations, followed by the retardation factor of the cut-off wall, the thickness and hydraulic conductivity of the lower cover layer, the hydraulic conductivity of the cut-off wall, and the thickness and hydraulic conductivity of the upper cover layer. Additionally, the proposed solution is used for the barrier system design of a mine legacy site. The minimum design thicknesses of the cut-off walls for three different cover system types and service times are obtained.